Many models of common human diseases and numerous traits of great biological interest vary among inbred strains of laboratory mice. Dissecting their multigenic control and identifying the responsible genes has been notoriously difficult. Chromosome substitution strains, which are a new paradigm for complex trait analysis, enable studies that are difficult or impossible with other genetic resources. CSSs involve a single chromosome substitution on a defined and inbred genetic background. In a CSS panel, each chromosome in the host strain is replaced with the corresponding chromosome from the donor strain. In genetically unique and statistically powerful ways, these CSSs facilitate detection of complex trait genes (QTLs), gene discovery and systems studies. In particular, the completed B6.A/J-Chr CSS panel enabled the first adequately powered study of the genetic architecture of complex traits in mammals. Studies in several laboratories showed that these QTLs in CSSs have unusually large phenotypic effects, that these effects are highly non-additive, and that congenics derived from CSSs provide a quick and reproducible way to reduce intervals to 1-5 candidate genes. CSS panels also have an attribute that is unique among QTL paradigms: a genome survey enables statistically robust phenotypic tests for individual genotypes, rather than average QTL effects across genetically heterogeneous populations. During the previous funding period, we finished several CSSs and made considerable progress towards completion of both the B6.129-Chr and 129.B6-Chr panels. In this application, we propose to bring to 19 the total number of completed CSSs in these two panels; the remaining 25 CSSs can then be completed within two years of the end of the proposed funding period. In addition, these will be the first reciprocal panels of CSSs that should enable unprecedented power to characterize gene interactions in reproducible manner, a task that is extremely challenging with any other paradigm. We also propose a pilot study to test the feasibility of using CSSs to test genetic modifiers for the Mecp2308 mutant mouse model of Rett Syndrome. This study would illustrate a new paradigm to identify and functionally characterize modifier genes and the functional networks in which they act. PUBLIC HEALTH RELEVANCE (provided by applicant): Characterizing the genetic control of mouse models for normal biological processes as well as common human diseases remains an enormous challenge because of multiple epistatic genes and with interactions between genetic and environmental factors. CSSs are a statistically powerful way to dissect the genetic control of these traits, simultaneously enabling gene discovery, functional studies, and systems analysis.